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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.